Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006737.1 Corchorus capsularis cultivar CVL-1 contig06758, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21560
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:6669 original size:57 final size:56
Alignment explanation
Indices: 6577--6697 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 56
6567 GATGACTTGA
* *
6577 ATAAATGATGAACAAAAAAAATCATAGAAGGATGAGTTGAAAGAGTGGTATTATCAC
1 ATAAATGATGAACAAAAAAAATCATAAAAGGATGAGTTGAAAGAGTGGTATGAT-AC
*** * *
6634 ATAAATGATGAACCCCAAAAGTCATAAAAGTATGAGTTGAAAGAGTGGTATGATAC
1 ATAAATGATGAACAAAAAAAATCATAAAAGGATGAGTTGAAAGAGTGGTATGATAC
*
6690 ATACATGA
1 ATAAATGA
6698 CCAATCCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 9 0.16
57 47 0.84
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (56 bp):
ATAAATGATGAACAAAAAAAATCATAAAAGGATGAGTTGAAAGAGTGGTATGATAC
Found at i:9052 original size:78 final size:78
Alignment explanation
Indices: 8964--9132 Score: 243
Period size: 78 Copynumber: 2.2 Consensus size: 78
8954 TTTTTTTAAT
* * * *
8964 TAAAATAGTAAAATGATAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAA-ATAG
1 TAAAATAGTAAAATGATAAAACAAAATAATTATAAAGATATTAGATTTAATTAAA-AAAAGATAA
9028 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
* * *
9042 TAAAATAGTAAAATGGTAAAACAAAATAATTATAAAGATATTAGATTTAGTTAAAAAAAGTTAAA
1 TAAAATAGTAAAATGATAAAACAAAATAATTATAAAGATATTAGATTTAATTAAAAAAAGATAAA
9107 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
9120 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
9133 GTTTAAACAA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
77 4 0.05
78 76 0.93
79 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.13, T:0.33
Consensus pattern (78 bp):
TAAAATAGTAAAATGATAAAACAAAATAATTATAAAGATATTAGATTTAATTAAAAAAAGATAAA
GTTTTTAGTTGAG
Found at i:9237 original size:6 final size:6
Alignment explanation
Indices: 9222--9286 Score: 96
Period size: 6 Copynumber: 11.0 Consensus size: 6
9212 TCTTTTTAAC
* * *
9222 ATAG-T ATAGAT ATAGAT ATAGAT ATCGAT ATTGAT ATAAAT ATAGAT
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT
9269 ATAGAT ATAGAT ATAGAT
1 ATAGAT ATAGAT ATAGAT
9287 TAACATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
5 4 0.07
6 50 0.93
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (6 bp):
ATAGAT
Found at i:9415 original size:14 final size:14
Alignment explanation
Indices: 9396--9426 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9386 TTCGACCTCA
9396 AAAATAAAAAAAAT
1 AAAATAAAAAAAAT
*
9410 AAAATAAATAAAAT
1 AAAATAAAAAAAAT
9424 AAA
1 AAA
9427 GGCCTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:9423 original size:9 final size:9
Alignment explanation
Indices: 9397--9426 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9387 TCGACCTCAA
*
9397 AAATAAAAA
1 AAATAAAAT
9406 AAATAAAAT
1 AAATAAAAT
9415 AAATAAAAT
1 AAATAAAAT
9424 AAA
1 AAA
9427 GGCCTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:14949 original size:51 final size:51
Alignment explanation
Indices: 14862--14969 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
14852 TTAATCCTCA
* * * * *
14862 ATTTGGCCTTTTAGTAATTTCCTATGTAGTTAAAAATGATATATAGTGTAT
1 ATTTGACCTTTTAGTAATTTCCTAGGTAGCTAAAAATAATATATAGTATAT
*
14913 ATTTGACCTTTTAGTAATTTCCCTAGGTA-CTGAAAATAATATATAGTATAT
1 ATTTGACCTTTTAGTAATTT-CCTAGGTAGCTAAAAATAATATATAGTATAT
14964 ATTTGA
1 ATTTGA
14970 TACATGTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 43 0.86
52 7 0.14
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (51 bp):
ATTTGACCTTTTAGTAATTTCCTAGGTAGCTAAAAATAATATATAGTATAT
Found at i:20510 original size:21 final size:22
Alignment explanation
Indices: 20473--20528 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
20463 TGAATGTAAG
*
20473 ATTACTAA-ATTTATTTATAAT-
1 ATTA-TAACATTTTTTTATAATC
*
20494 ATTATAACTTTTTTTTATAATC
1 ATTATAACATTTTTTTATAATC
*
20516 TTTATAACATTTT
1 ATTATAACATTTT
20529 CTGAAAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
22 11 0.38
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATAACATTTTTTTATAATC
Done.